I didn't have played with WebAudio yet, but I assume that the main problem of HTML5 <audio/> is that the controls cannot be customized to fit the stylesheet. Using WebAudio probably allows to use custom html structure.
So the main question is : when will we have a standard shadow dom styling ? :(
You can do any customization with <audio/> that you can with Web Audio. The element doesn't have to be in the DOM to play audio.
It's actually harder to provide custom UI for the Web Audio API since seeking and general stream navigation are a complete afterthought and their API makes them a pain.
So the main question is : when will we have a standard shadow dom styling ? :(